VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Mar 20 2008 - 17:03:47 CDT

Hi,
  Are you running your machine out of memory with the larger
structures? It definitely shouldn't get "stuck", as there's nothing
I saw in Axel's example script that would seem to grow in a non-linear
fashion with regard to the number of atoms or number of frames. That
said however, if you're on the edge of running your system out of
memory, that would explain the sort of behavior you describe.
If you're running Windows or MacOS, you can check your system's
memory utilization with little utilities provided by the OS, on
Unix/Linux you can use "top" to see how much memory you have left.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Mar 20, 2008 at 05:50:50PM -0400, Simone Melchionna wrote:
> Hi all,
>
> I am trying to visualize atoms with dynamically changing colors and used
> the script in
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3
> However, when trying to visualize large number of atoms (~ 5000) vmd
> runs extremely slow. Above 10,000 atoms it seems to get stuck.
> Is there a better way to attaching external properties e.g. by including
> them directly to the frames?
>
> Thanks,
> Simone 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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